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The story picks up from the ending of Sonic 3 - Dr. Robotnik's orbital weapon, the Death Egg, has been badly damaged in the climactic battle between himself and Sonic the Hedgehog. As the satellite falls back to Floating Island,[3] landing in a volcanic crater, Sonic jumps off, landing in a mushroom filled woodland.

Sonic knows there are many Chaos Emeralds hidden on the island, including the powerful Master Emerald, the secret to the island's levitation powers. Worried that Robotnik may try to harness this power to fuel a repaired Death Egg, he sets off to try and destroy it once and for all, keeping an eye out for Knuckles the Echidna, still smarting from his Launch Base defeat.

Meanwhile, as Robotnik begins repairing the Death Egg, he decides that Knuckles has served his purpose, and dispatches an EggRobo, a highly autonomous robot built in his own image, to dispose of Knuckles. He assumes that if EggRobo can't destroy Knuckles, his cover as the real mastermind won't be blown, leaving the possibility that Sonic and Knuckles may fight to the death. EggRobo's first assassination attempt - Dropping a bomb on a half-asleep Knuckles - only serves to enrage the echidna, setting him on a mission to stop both Sonic, his mystery assailant and Robotnik from getting the Master Emerald. EggRobo is eventually destroyed in Knuckles' confrontation with Metal Sonic, charged with the power of the Master Emerald in an attempt to destroy Knuckles and Angel Island in one blow. [4]

Gameplay focuses on Sonic and Knuckles, Knuckles not being playable in Sonic the Hedgehog 3 because of Knuckles' role as an antagonist towards Sonic and Tails. In addition, Tails has now been removed from play. Essentially there are two separate games to tackle, depending on which character is selected at the start of the game. Although the appearance of the Zones is the same for either character, their layout and some of the bosses' tricks differs noticeably at a number of points in the game (an especially noticeable difference is that Knuckles fights EggRobo, who has different and particularly smarter strategies). Zone differences increase starting from the Lava Reef Zone onwards. Style of play, however, does not differ significantly from one character to the next as it does, for example, in Sonic Adventure.

Despite no save file slots, gameplay is much expanded than in other games, as Sonic and Knuckles do not play all of the same levels. A significant difference between Sonic and Knuckles is that they don't have all of the same moves: Sonic can jump higher and run a little faster than Knuckles, and Sonic has the Insta-Shield, while Knuckles can climb walls and break through some of the blocked entry ways using his strong fists. While Sonic has the gift of speed, Knuckles can glide through the air with the greatest of ease.

As in Sonic the Hedgehog 3, there are two types of Stages: Bonus Stages and Special Stages. The Bonus Stages are entered by collecting at least 20 rings (or at least 50 to access the second Bonus Stage), and jumping through the bright ring of stars that appears above each checkpoint in the Zones. This time however, the gumball stage has been replaced by two new Bonus Stages. The first combines the slot machines of Sonic the Hedgehog 2's Casino Night Zone and the 360° tumbling labyrinth Special Stage (to retrieve the Chaos Emeralds) of the first Sonic the Hedgehog. If three Robotniks appear on the slot machine, the player will lose 100 rings, or all the rings below 100. The second Bonus Stage is a large vertical course, with magnetic orbs that Sonic can use to propel himself upward. Along the way he can pick up shields, rings or lives. He is chased by a horizontal force field that slowly moves up and, when Sonic is caught in it, ends the stage, and reaching the top of the stage ends it as well.

Sonic & Knuckles utilizes "lock-on technology" that lets the cartridge plus the Genesis/Mega Drive access data from Sonic the Hedgehog 2 and Sonic the Hedgehog 3 so that elements of both Sonic & Knuckles and the locked-on game are combined. To play these combined games, the hatch on top of the Sonic & Knuckles cartridge can be flipped open and the second game placed inside.

The lock-on technology was actually a way of making up for the fact that the developers could not meet the deadline for Sonic 3. Originally, Sonic 3 was to be released with Knuckles as a playable character, and with all the Sonic & Knuckles levels playable (the level select screen in Sonic 3 features inaccessible Sonic & Knuckles levels and music for said levels can be played in the sound test; the Knuckles-only routes through the Sonic 3 levels can also be accessed via the debug mode). Time constraints forced them to split the project in two, releasing Sonic 3 with the completed levels and continuing work on the uncompleted ones, plus adding the Super Emeralds, and the lock-on feature. Indeed Sonic 2 had once run into similar problems, resulting in the original Hidden Palace and several other levels being removed.[5]

This kind of “lock-on” functionality is rarely seen elsewhere in video game history. Some Konami games for the MSX can be combined with another in the computer’s secondary cartridge slot to unlock certain small visual changes and cheats [1], and combining Salamander with Nemesis 2 unlocks an entire level. Some NES games released by HES, as well as the Super Nintendo game Super 3D Noah's Ark, feature a cartridge port on the top to accept other games for the system, but this was purely to override the systems' respective lockout chips, as these games were not licensed by Nintendo. Some video game peripherals require being joined with a cartridge in a similar manner (i.e. Game Genie; GameShark), or transfer data between games (the Transfer Pak) but don't allow the "lock on"-style merging of data from 2 different video games.

Also known as Sonic 3 & Knuckles; there are seven immediate differences:

The player can play as Knuckles in the Sonic 3 levels.

The player can play as Tails in the Sonic & Knuckles levels or have Tails follow Sonic throughout the entire game.

After the levels of Sonic 3 are finished, the Death Egg was seen to fall intact instead of being destroyed, the player continues straight to the levels of Sonic & Knuckles. The final boss of Sonic 3 is also omitted for Sonic and Tails.

Players must collect each Chaos Emerald before the correspondingly colored Super Emerald can be collected.

Game progress can be saved in Sonic & Knuckles using Sonic 3's save feature (there are now 8 rather than 6 save slots).

Save slots now display information about the number of continues, lives, and the Chaos Emeralds surround the player's character as the player collects them (the Chaos Emeralds are replaced with the correspondingly colored Super Emeralds when the player collects them).

The game uses Sonic & Knuckles' sound bank exclusively with the exception of the Sonic 3 levels' BGM, which means that the songs that were different between Sonic 3 and Sonic & Knuckles (which include the title screen, 1-up, and invincibility sounds, as well as the mid-level boss music, Knuckles' theme and end credits theme) use only the Sonic & Knuckles version.

Once the player picks a character and starts playing, more differences become apparent. Passing a star post can now open up all 3 Bonus Stages, including the slot machine stage (20-34 rings required), the magnetic orbs stage (35–49 rings required) from Sonic & Knuckles as well as the gumball machine (50–65 rings required) from Sonic 3. Knuckles' levels are different from Sonic's and Tails' in most cases, with new areas and bosses. There are slight differences in object placement in some of the Sonic 3 Zones as well (Launch Base in particular). Sonic and Tails skips the final boss of Launch Base, while Knuckles still has to do it (although he skips the first true boss of Launch Base). The Sonic & Knuckles levels are the same, except that Mushroom Hill now has an intro (Tails airlifts Sonic in).

Collecting all the Chaos Emeralds in the Sonic 3 levels will turn Sonic or Knuckles into Super Sonic or Super Knuckles. However, once the player enters their first Special Stage in Mushroom Hill Zone, they teleport to Hidden Palace where the Emeralds are taken from them and transformed into gray Super Emeralds, thus beginning the Super Emerald quest. If the player does not have all of the Chaos Emeralds prior to reaching Mushroom Hill, the acquired Chaos Emeralds will become Super Emeralds and the player is given the opportunity to acquire the first Super Emerald. However, the player will not be allowed to return to Hidden Palace via warp rings until they collect the remaining Chaos Emeralds. In addition, both Knuckles and Sonic can now go Hyper once they have obtained all of the Super Emeralds.

Tails cannot normally gain Emerald powers but does so when he collects all Super Emeralds, taking on the form of Super Tails. He has no Hyper form but simply remains Super, with four Super Flickies flying around him that attack nearby enemies. Taking care to avoid all the Special Stages in the latter half of the game, it is possible to finish the game with only the 7 Chaos Emeralds, retaining their Super powers (but not gaining Hyper powers) until the very end of the game. In this case the game endings will resemble the good endings from Sonic & Knuckles. This allows for a total of nine different endings — each character (Sonic and Tails together have the same as Sonic alone) has one with 0–6 Chaos Emeralds, one with all 7 Chaos Emeralds and 0-6 Super Emeralds, and the third with all 14 Chaos and Super Emeralds.
This game was originally going to be Sonic the Hedgehog 3 when Sonic 3 was in development, but it was too much data and they couldn't have finished in time, so they split the game in two, released Sonic 3, and worked on Sonic and Knuckles.

Also known as Knuckles the Echidna in Sonic the Hedgehog 2 (or Knuckles in Sonic 2 for short), this game is identical to Sonic 2 (aside from a few changes to make it more playable with Knuckles) but with Knuckles now playable instead of Sonic or Tails. The title screen features Knuckles and the only option is "Press Start" (Options and the versus mode have been disabled). There are no new Zones. The only differences in gameplay is that Knuckles can explore once inaccessible areas (where secrets such as 1-ups have been added for Knuckles), some areas are harder because Knuckles cannot jump very high and accelerates slowly (in particular, the final boss of Sonic 2, the giant robot in Death Egg Zone, is regarded as being much more difficult to beat while playing as Knuckles because of his weaker jumping ability), the title cards (ex. Emerald Hill Zone Act 1) are green and red, shields are now gray, and Knuckles retains his rings after a Special Stage, making it much easier to obtain Chaos Emeralds. Getting the Emeralds is easier too, for the Special Stages have reduced Ring quotas for Knuckles making it much easier to obtain Super Knuckles.

Unlike the Sonic 3 lock-on, where the Sonic & KnucklesROM referenced the data in Sonic 3 to add its additional features, this game used the Sonic 2 data bank exclusively except for an otherwise hidden extra data bank on the Sonic & Knuckles cart. The lack of knowledge over the existence of this patch made it impossible to find a working dump of the Knuckles in Sonic 2 ROM for a long time.

In the development of Sonic & Knuckles, Sega attempted to implement Knuckles into the original game, but decided to leave him out. According to several programmers and hackers, the reason why Knuckles could not be placed into Sonic the Hedgehog like he was in Sonic 2 was that the palette colors of Knuckles' sprite would have, in fact, completely altered the palette scheme of the entire game. Therefore, instead of a Knuckles in Sonic 1 feature, fans were treated to a full version of the Blue Sphere game (see below). Hackers, however, succeeded several years later in making a game hack called Knuckles the Echidna in Sonic the Hedgehog.[2] The color palette problems were overcome by reusing the shoe colors (two shades of pure red) for Knuckles' body, instead of the original three shades of pinkish-red, and changing his socks from green to blue, so that the palette did not have to change.

By placing the first Sonic game, or most other Genesis/Mega Drive games inside, a "No way? No way!" screen will pop up with Sonic, Tails, Knuckles, and Robotnik making odd postures, telling the player that the cartridge is supposedly incompatible. But, by pressing the A, B, and C buttons together, a minigame based on the Chaos Emerald bonus levels is unlocked, called "Blue Sphere". There are over 100 million unique levels. The last level, "Special Stage", repeats itself once the level is beaten. Only by locking the original Sonic the Hedgehog or Sonic Compilation in the Sonic & Knuckles cart can one play through all the stages. The other Genesis/Mega Drive games will only play one level each, which will infinitely repeat. Despite being near randomly generated, the levels are playable for the most part, even if many bits and pieces of levels get recycled. On another note, some levels may be nearly impossible to complete while others are not as difficult.

In Sonic Jam and Sonic Mega Collection, Blue Sphere is playable as a separate game. Sonic Jam allows the player to access it by choosing to play Sonic & Knuckles and "lock it on" with Sonic 1. In Mega Collection, the game has to be unlocked separately. Additionally, there was a PC CD-ROM released, entitled Sonic & Knuckles Collection, that contained Sonic & Knuckles, Sonic 3, as well as the pre-combined version of the two games. This CD-ROM contained a full version of Blue Sphere.

Playing these levels via a game with a battery pack has been known to erase saved games. Additionally, games made after Sonic & Knuckles was released will not work with its lock-on feature. There are only a few games made before Sonic & Knuckles that do not work, such as Phantasy Star IV & the Mega Drive/Genesis port of Super Street Fighter II.
The reason that these games are unable to work with Sonic & Knuckles is that the combined size of the two games' data exceeds 4 megabytes, which is the maximum amount of memory that the Genesis/Mega Drive allots for game data.

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Prior to the release of Sonic & Knuckles in North America, Blockbuster Video and MTV co-sponsored a tournament contest where kids were allowed to play a pre-release of the game, leading to a final tournament held at Alcatraz Island in San Francisco, California. A special on the game showing the tournament final, "MTV's Rock the Rock Warning", was aired shortly before the game's release.